Query psy822
Match_columns 190
No_of_seqs 155 out of 525
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 21:43:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy822.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/822hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3183|consensus 100.0 8.7E-44 1.9E-48 305.1 1.6 161 1-161 2-168 (250)
2 PF01428 zf-AN1: AN1-like Zinc 99.3 9.8E-13 2.1E-17 86.0 2.4 41 10-50 1-41 (43)
3 PF01428 zf-AN1: AN1-like Zinc 99.2 3.4E-12 7.4E-17 83.4 2.1 40 100-139 1-40 (43)
4 smart00154 ZnF_AN1 AN1-like Zi 99.2 1.2E-11 2.7E-16 79.7 2.7 34 14-47 3-37 (39)
5 smart00154 ZnF_AN1 AN1-like Zi 98.9 5.6E-10 1.2E-14 72.0 2.5 33 105-137 4-37 (39)
6 KOG3183|consensus 97.8 6E-06 1.3E-10 72.1 1.1 41 97-137 8-48 (250)
7 COG3582 Predicted nucleic acid 97.8 1.4E-05 2.9E-10 66.2 2.6 132 14-152 5-150 (162)
8 KOG3173|consensus 97.3 0.00025 5.5E-09 58.8 3.4 51 97-150 105-156 (167)
9 COG3582 Predicted nucleic acid 94.6 0.018 3.8E-07 47.9 1.6 38 14-51 102-139 (162)
10 KOG3173|consensus 93.3 0.043 9.4E-07 45.5 1.5 31 16-47 113-143 (167)
11 PF04236 Transp_Tc5_C: Tc5 tra 88.5 0.39 8.5E-06 34.1 2.3 39 4-44 24-63 (63)
12 PF04236 Transp_Tc5_C: Tc5 tra 87.0 0.38 8.2E-06 34.1 1.5 36 97-134 27-63 (63)
13 smart00734 ZnF_Rad18 Rad18-lik 82.6 0.42 9.1E-06 28.1 0.1 20 55-81 2-21 (26)
14 PF13465 zf-H2C2_2: Zinc-finge 77.5 0.93 2E-05 26.2 0.4 12 21-32 13-24 (26)
15 PF13912 zf-C2H2_6: C2H2-type 74.8 1.2 2.6E-05 25.2 0.4 12 22-33 1-12 (27)
16 PF05605 zf-Di19: Drought indu 71.7 2.1 4.6E-05 28.5 1.1 34 23-63 3-40 (54)
17 PF01485 IBR: IBR domain; Int 71.4 3.3 7.2E-05 27.3 2.0 33 98-130 19-58 (64)
18 KOG1813|consensus 70.8 2.1 4.4E-05 39.1 1.1 49 17-65 236-286 (313)
19 PRK00398 rpoP DNA-directed RNA 60.4 7.1 0.00015 25.2 1.9 34 21-68 2-35 (46)
20 smart00647 IBR In Between Ring 58.9 7.1 0.00015 25.7 1.8 33 98-130 19-58 (64)
21 PF06524 NOA36: NOA36 protein; 55.1 6.7 0.00015 35.5 1.4 52 14-70 163-225 (314)
22 PF07975 C1_4: TFIIH C1-like d 53.4 5.3 0.00011 27.3 0.4 26 20-45 19-47 (51)
23 PF00096 zf-C2H2: Zinc finger, 52.2 5.8 0.00013 21.4 0.4 8 57-64 3-10 (23)
24 PF06006 DUF905: Bacterial pro 52.0 25 0.00054 25.6 3.7 37 142-186 10-46 (70)
25 PF09723 Zn-ribbon_8: Zinc rib 51.3 10 0.00022 24.3 1.4 30 22-62 5-34 (42)
26 PLN03086 PRLI-interacting fact 49.2 9.2 0.0002 37.6 1.4 11 22-32 453-463 (567)
27 PHA00616 hypothetical protein 49.0 5.4 0.00012 26.5 -0.1 12 22-33 1-12 (44)
28 PF13717 zinc_ribbon_4: zinc-r 47.3 8.5 0.00019 24.0 0.6 16 55-70 3-18 (36)
29 PF13894 zf-C2H2_4: C2H2-type 45.3 9.5 0.00021 20.0 0.5 8 57-64 3-10 (24)
30 KOG2462|consensus 45.2 9.5 0.00021 34.4 0.8 60 21-86 186-269 (279)
31 PF13719 zinc_ribbon_5: zinc-r 43.7 9.5 0.00021 23.8 0.4 16 55-70 3-18 (37)
32 smart00834 CxxC_CXXC_SSSS Puta 43.6 17 0.00037 22.2 1.6 31 23-64 6-36 (41)
33 TIGR00599 rad18 DNA repair pro 42.8 11 0.00023 35.6 0.7 26 55-87 182-207 (397)
34 PF14169 YdjO: Cold-inducible 42.4 15 0.00032 25.9 1.3 16 52-67 37-52 (59)
35 PHA02768 hypothetical protein; 41.8 11 0.00024 26.1 0.5 13 20-32 3-15 (55)
36 PF14634 zf-RING_5: zinc-RING 40.3 12 0.00027 23.7 0.6 31 22-62 14-44 (44)
37 KOG1701|consensus 38.6 18 0.00038 34.8 1.5 47 18-76 370-416 (468)
38 PRK00415 rps27e 30S ribosomal 38.3 20 0.00044 25.2 1.4 42 18-72 7-48 (59)
39 TIGR02098 MJ0042_CXXC MJ0042 f 37.7 15 0.00033 22.5 0.7 34 23-65 3-36 (38)
40 KOG4739|consensus 35.9 23 0.0005 31.2 1.7 37 20-68 15-51 (233)
41 TIGR02605 CxxC_CxxC_SSSS putat 34.6 27 0.00058 22.7 1.5 29 23-62 6-34 (52)
42 COG5222 Uncharacterized conser 33.9 19 0.00042 33.3 1.0 63 1-74 268-330 (427)
43 COG2051 RPS27A Ribosomal prote 32.3 23 0.0005 25.6 0.9 42 18-72 15-56 (67)
44 PF04423 Rad50_zn_hook: Rad50 30.0 18 0.00038 24.1 0.0 10 56-65 22-31 (54)
45 PF09538 FYDLN_acid: Protein o 28.5 40 0.00086 26.1 1.8 26 98-125 10-39 (108)
46 PHA02565 49 recombination endo 27.8 37 0.00079 28.3 1.6 39 24-66 22-67 (157)
47 smart00355 ZnF_C2H2 zinc finge 27.4 25 0.00054 18.3 0.4 6 57-62 3-8 (26)
48 PF02176 zf-TRAF: TRAF-type zi 27.3 16 0.00036 24.0 -0.5 26 54-86 9-36 (60)
49 PF11290 DUF3090: Protein of u 26.3 33 0.00072 28.9 1.0 11 54-64 154-164 (171)
50 PRK00418 DNA gyrase inhibitor; 26.2 50 0.0011 23.5 1.8 14 53-66 5-18 (62)
51 PF10571 UPF0547: Uncharacteri 25.9 51 0.0011 19.3 1.5 18 105-122 6-24 (26)
52 PF04438 zf-HIT: HIT zinc fing 25.0 39 0.00084 20.4 0.9 19 14-34 7-25 (30)
53 PF12230 PRP21_like_P: Pre-mRN 24.6 25 0.00054 29.8 0.0 23 53-82 167-189 (229)
54 smart00451 ZnF_U1 U1-like zinc 24.1 36 0.00077 19.9 0.6 8 57-64 6-13 (35)
55 PF13913 zf-C2HC_2: zinc-finge 24.0 34 0.00073 19.6 0.5 10 113-122 3-12 (25)
56 COG3024 Uncharacterized protei 23.9 44 0.00096 24.0 1.2 17 51-67 4-20 (65)
57 TIGR03847 conserved hypothetic 23.8 39 0.00085 28.7 1.0 11 54-64 156-166 (177)
58 COG0846 SIR2 NAD-dependent pro 23.5 52 0.0011 29.0 1.8 38 18-63 118-155 (250)
59 KOG2462|consensus 22.5 38 0.00083 30.6 0.8 25 22-46 215-248 (279)
60 cd00065 FYVE FYVE domain; Zinc 22.4 52 0.0011 21.3 1.3 25 14-38 7-34 (57)
61 PLN00209 ribosomal protein S27 22.4 52 0.0011 24.9 1.4 41 19-72 33-73 (86)
62 PF12171 zf-C2H2_jaz: Zinc-fin 21.8 46 0.001 18.8 0.8 21 56-82 3-23 (27)
63 COG1996 RPC10 DNA-directed RNA 21.7 50 0.0011 22.4 1.1 33 21-67 5-37 (49)
64 PTZ00083 40S ribosomal protein 21.5 56 0.0012 24.7 1.4 41 19-72 32-72 (85)
65 TIGR02174 CXXU_selWTH selT/sel 21.5 84 0.0018 22.1 2.3 27 151-188 29-55 (72)
66 PRK03824 hypA hydrogenase nick 21.1 77 0.0017 25.1 2.2 48 21-71 69-125 (135)
67 PHA00732 hypothetical protein 20.9 41 0.00089 24.5 0.5 12 22-33 1-12 (79)
68 PF13842 Tnp_zf-ribbon_2: DDE_ 20.9 69 0.0015 19.5 1.5 16 111-126 15-30 (32)
69 cd00350 rubredoxin_like Rubred 20.8 89 0.0019 18.8 2.0 8 55-62 18-25 (33)
70 TIGR00595 priA primosomal prot 20.8 76 0.0016 30.4 2.5 22 98-121 241-262 (505)
71 PF02891 zf-MIZ: MIZ/SP-RING z 20.1 20 0.00044 23.8 -1.1 9 55-63 42-50 (50)
72 TIGR00622 ssl1 transcription f 20.0 57 0.0012 25.7 1.2 15 22-36 81-95 (112)
No 1
>KOG3183|consensus
Probab=100.00 E-value=8.7e-44 Score=305.14 Aligned_cols=161 Identities=50% Similarity=0.987 Sum_probs=142.4
Q ss_pred CCCCCCCCCCCcCCCCCccccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCcchhhcccc
Q psy822 1 MEFPHLGKHCSIETCKKLDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELPDFAVGLHI 80 (190)
Q Consensus 1 MEf~diG~hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~pn~~v~~Hi 80 (190)
|||||||+||++++|+|||||||+|+.|+..||+|||++++|.|+.+...|++|++||+|++||++.+++.++.+|+.|+
T Consensus 2 ~efpDlGkHCs~~~CkqlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~~de~~~~~v~~h~ 81 (250)
T KOG3183|consen 2 MEFPDLGKHCSVPYCKQLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTKKDEAPDKVVEPHI 81 (250)
T ss_pred CcccccccccCcchhhhccccceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCCCCcchhhhhchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCchHHhhhccccCCCcCCCCCcCccCc--ccCcccCccccccCcCCCCCCCCc-cchHHHHHHHHH---hhhhhh
Q psy822 81 DNNCDSDTAQERRKIFTNKCSVKNCKGKELIP--VKCYQCAMNFCLKHRHPNDHKCEG-QKNAARNKALLK---MKLWHE 154 (190)
Q Consensus 81 ~~~C~~~~~~kk~k~~~~~Cs~~~Ck~~~~~~--~~C~~C~~~FClkHR~p~dH~C~~-~~~~~~~~a~~k---~~~w~~ 154 (190)
+++|+..+..+++++++++|+.++|++++.+. |.|.+|+.+||++||++.||.|.. ++.+...+.+++ +..|+.
T Consensus 82 ~~dC~~~~~~~~~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~~~~~~~k~~a~~~~~~~~q~~~~ 161 (250)
T KOG3183|consen 82 SNDCDRHPEQKKRKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCNKQLGNLKKKAGGDKIGPMQNRIY 161 (250)
T ss_pred ccccccCchhhhcccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhhhhccCccccccccccccccceee
Confidence 99999988887888999999999999998766 999999999999999999999993 443322333333 345555
Q ss_pred hcccccc
Q psy822 155 LSNYQCK 161 (190)
Q Consensus 155 ~~~~~~~ 161 (190)
--+|..+
T Consensus 162 ~~~~~~~ 168 (250)
T KOG3183|consen 162 IWTYLSS 168 (250)
T ss_pred eeEeecC
Confidence 5555544
No 2
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.30 E-value=9.8e-13 Score=85.98 Aligned_cols=41 Identities=44% Similarity=0.899 Sum_probs=31.3
Q ss_pred CCcCCCCCccccceeccccccccccCCCCCCCccCCccccc
Q psy822 10 CSIETCKKLDFLPVKCDACLEMFCSDHMSYVGHQCKSAARK 50 (190)
Q Consensus 10 C~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~ 50 (190)
|++++|+++|||||+|+.|++.||.+||.+++|+|++...+
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccCCCeECCCCCcccCccccCccccCCcchhhc
Confidence 78899999999999999999999999999999999976543
No 3
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.23 E-value=3.4e-12 Score=83.42 Aligned_cols=40 Identities=48% Similarity=1.138 Sum_probs=30.7
Q ss_pred CcCCCCCcCccCcccCcccCccccccCcCCCCCCCCccch
Q psy822 100 CSVKNCKGKELIPVKCYQCAMNFCLKHRHPNDHKCEGQKN 139 (190)
Q Consensus 100 Cs~~~Ck~~~~~~~~C~~C~~~FClkHR~p~dH~C~~~~~ 139 (190)
|++++|++++++++.|+.|++.||++||+|++|.|.....
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~ 40 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLKHRLPEDHNCSKLQK 40 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TTTHSTTTCT-SSTTS
T ss_pred CccCcCcCccCCCeECCCCCcccCccccCccccCCcchhh
Confidence 7889999999999999999999999999999999998654
No 4
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.18 E-value=1.2e-11 Score=79.73 Aligned_cols=34 Identities=32% Similarity=0.674 Sum_probs=32.5
Q ss_pred CCCCcccc-ceeccccccccccCCCCCCCccCCcc
Q psy822 14 TCKKLDFL-PVKCDACLEMFCSDHMSYVGHQCKSA 47 (190)
Q Consensus 14 ~C~qlDFL-Pf~C~~C~~~FC~eHr~~~~H~C~~~ 47 (190)
.|+++||| ||+|++|++.||++||.+++|+|+..
T Consensus 3 ~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~ 37 (39)
T smart00154 3 FCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGD 37 (39)
T ss_pred ccCCcccccCeECCccCCccccccCCccccCCccc
Confidence 69999999 99999999999999999999999864
No 5
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=98.93 E-value=5.6e-10 Score=72.00 Aligned_cols=33 Identities=42% Similarity=0.954 Sum_probs=31.1
Q ss_pred CCcCccC-cccCcccCccccccCcCCCCCCCCcc
Q psy822 105 CKGKELI-PVKCYQCAMNFCLKHRHPNDHKCEGQ 137 (190)
Q Consensus 105 Ck~~~~~-~~~C~~C~~~FClkHR~p~dH~C~~~ 137 (190)
|++++.+ +++|+.|++.||++||+|++|+|+.+
T Consensus 4 C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~ 37 (39)
T smart00154 4 CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGD 37 (39)
T ss_pred cCCcccccCeECCccCCccccccCCccccCCccc
Confidence 8999888 99999999999999999999999865
No 6
>KOG3183|consensus
Probab=97.82 E-value=6e-06 Score=72.08 Aligned_cols=41 Identities=39% Similarity=0.873 Sum_probs=38.5
Q ss_pred cCCCcCCCCCcCccCcccCcccCccccccCcCCCCCCCCcc
Q psy822 97 TNKCSVKNCKGKELIPVKCYQCAMNFCLKHRHPNDHKCEGQ 137 (190)
Q Consensus 97 ~~~Cs~~~Ck~~~~~~~~C~~C~~~FClkHR~p~dH~C~~~ 137 (190)
...|+.+.|++.+++||+|..|+..||+.||.-++|+|...
T Consensus 8 GkHCs~~~CkqlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~ 48 (250)
T KOG3183|consen 8 GKHCSVPYCKQLDFLPFKCDGCSGIFCLEHRSYESHHCPKG 48 (250)
T ss_pred ccccCcchhhhccccceeeCCccchhhhccchHhhcCCCcc
Confidence 35899999999999999999999999999999999999875
No 7
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=97.79 E-value=1.4e-05 Score=66.25 Aligned_cols=132 Identities=17% Similarity=0.244 Sum_probs=72.0
Q ss_pred CCCCccccceeccccccccccCCCCCCCccCCcccc-cccccc---cCCCCCCCccCCCCCCcchhhcccccCCCCC---
Q psy822 14 TCKKLDFLPVKCDACLEMFCSDHMSYVGHQCKSAAR-KDIQVP---VCPLCNQPVPTKRGELPDFAVGLHIDNNCDS--- 86 (190)
Q Consensus 14 ~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~-~d~~v~---~CPlC~~~V~~~~g~~pn~~v~~Hi~~~C~~--- 86 (190)
++....=||++|+.+.+.|+.+|+..-.|.++.... +|+.-+ -=-.+.+-+++-. .....++.+ ++..
T Consensus 5 s~~~~~~lP~r~~~~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~~~~~~~~p~i~--~~~~~~~~~---~~~k~s~ 79 (162)
T COG3582 5 SRVSETRLPSRGNITAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDPGQAMKCLPLIS--SAVSNPSNT---DTPKRST 79 (162)
T ss_pred ccceeccCCccccceeeeccCccccccccccchhhhhhhhhccccCCCcchhhhcceEE--EEeeccccc---cCccccc
Confidence 344455699999999999999999999999985310 110000 0000001111000 000001111 1110
Q ss_pred -----chHHhhhccccCCCcCCCCCcC-ccCcccCcccCccccccCcCCCCCCCCccchHHHHHH-HHHhhhh
Q psy822 87 -----DTAQERRKIFTNKCSVKNCKGK-ELIPVKCYQCAMNFCLKHRHPNDHKCEGQKNAARNKA-LLKMKLW 152 (190)
Q Consensus 87 -----~~~~kk~k~~~~~Cs~~~Ck~~-~~~~~~C~~C~~~FClkHR~p~dH~C~~~~~~~~~~a-~~k~~~w 152 (190)
.+...... ...+|....|..+ +.++..|+.|+..||..||+++.|+|..+.. .+... +.+..+|
T Consensus 80 ~~~~~~~~~~~~~-~t~~~a~~~~~g~~s~l~~~c~~c~g~fc~~h~lp~nhdc~~L~s-~r~~~~ip~~~~~ 150 (162)
T COG3582 80 RVPLNGPFDSGKG-ITDRCATPQCTGKGSTLAGKCNYCTGYFCAEHRLPENHDCNGLGS-LRVTFVIPRNVIP 150 (162)
T ss_pred ccccccccccccc-cceeeecceeccCCccccccccCCCCcceeceecccccccccHHH-hhhhcCCCCCcee
Confidence 01000111 1236666555544 6678999999999999999999999988765 33332 4444444
No 8
>KOG3173|consensus
Probab=97.25 E-value=0.00025 Score=58.78 Aligned_cols=51 Identities=31% Similarity=0.696 Sum_probs=41.4
Q ss_pred cCCCcCCCCCcC-ccCcccCcccCccccccCcCCCCCCCCccchHHHHHHHHHhh
Q psy822 97 TNKCSVKNCKGK-ELIPVKCYQCAMNFCLKHRHPNDHKCEGQKNAARNKALLKMK 150 (190)
Q Consensus 97 ~~~Cs~~~Ck~~-~~~~~~C~~C~~~FClkHR~p~dH~C~~~~~~~~~~a~~k~~ 150 (190)
.++|-. |+++ .+..|.| .|+..||..||+++.|+|.-......+.+|.|+.
T Consensus 105 ~~rC~~--C~kk~gltgf~C-rCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~n 156 (167)
T KOG3173|consen 105 KKRCFK--CRKKVGLTGFKC-RCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKAN 156 (167)
T ss_pred chhhhh--hhhhhccccccc-ccCCcccccccCCccccccccHHHHHHHHHHHhC
Confidence 456776 6655 5567999 8999999999999999999988877777777753
No 9
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=94.59 E-value=0.018 Score=47.92 Aligned_cols=38 Identities=26% Similarity=0.493 Sum_probs=33.7
Q ss_pred CCCCccccceeccccccccccCCCCCCCccCCcccccc
Q psy822 14 TCKKLDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKD 51 (190)
Q Consensus 14 ~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d 51 (190)
.|+.---||++|++|+..||.+|+.++.|.|..+..+.
T Consensus 102 ~~g~~s~l~~~c~~c~g~fc~~h~lp~nhdc~~L~s~r 139 (162)
T COG3582 102 CTGKGSTLAGKCNYCTGYFCAEHRLPENHDCNGLGSLR 139 (162)
T ss_pred eccCCccccccccCCCCcceeceecccccccccHHHhh
Confidence 56677889999999999999999999999999876653
No 10
>KOG3173|consensus
Probab=93.28 E-value=0.043 Score=45.54 Aligned_cols=31 Identities=32% Similarity=0.645 Sum_probs=26.9
Q ss_pred CCccccceeccccccccccCCCCCCCccCCcc
Q psy822 16 KKLDFLPVKCDACLEMFCSDHMSYVGHQCKSA 47 (190)
Q Consensus 16 ~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~ 47 (190)
.++....|.|. |+.+||..||.++.|.|.--
T Consensus 113 kk~gltgf~Cr-CG~~fC~~HRy~e~H~C~fD 143 (167)
T KOG3173|consen 113 KKVGLTGFKCR-CGNTFCGTHRYPEQHDCSFD 143 (167)
T ss_pred hhhcccccccc-cCCcccccccCCcccccccc
Confidence 45667789997 99999999999999999843
No 11
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=88.46 E-value=0.39 Score=34.07 Aligned_cols=39 Identities=26% Similarity=0.751 Sum_probs=32.9
Q ss_pred CCCCCCCCcCCCCCccccceeccccccccccCCCCC-CCccC
Q psy822 4 PHLGKHCSIETCKKLDFLPVKCDACLEMFCSDHMSY-VGHQC 44 (190)
Q Consensus 4 ~diG~hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~-~~H~C 44 (190)
.+....|..++|+.+-| ++|.+|.+.+|-+|+-. +-|.|
T Consensus 24 ~~~~~~C~~~gC~~~s~--I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 24 KNVAGDCDITGCNNTSF--IRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred CCCcCcCCCCCCCCcCE--EEccccCCcccccceeeeeeEcC
Confidence 34556899899999998 58999999999999995 67776
No 12
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=87.04 E-value=0.38 Score=34.14 Aligned_cols=36 Identities=22% Similarity=0.784 Sum_probs=29.1
Q ss_pred cCCCcCCCCCcCccCcccCcccCccccccCcCC-CCCCC
Q psy822 97 TNKCSVKNCKGKELIPVKCYQCAMNFCLKHRHP-NDHKC 134 (190)
Q Consensus 97 ~~~Cs~~~Ck~~~~~~~~C~~C~~~FClkHR~p-~dH~C 134 (190)
...|...+|+...+ ++|..|++.+|.+|-+- +-|.|
T Consensus 27 ~~~C~~~gC~~~s~--I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 27 AGDCDITGCNNTSF--IRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred cCcCCCCCCCCcCE--EEccccCCcccccceeeeeeEcC
Confidence 45788899996554 59999999999999995 56665
No 13
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=82.61 E-value=0.42 Score=28.12 Aligned_cols=20 Identities=35% Similarity=0.855 Sum_probs=15.0
Q ss_pred ccCCCCCCCccCCCCCCcchhhccccc
Q psy822 55 PVCPLCNQPVPTKRGELPDFAVGLHID 81 (190)
Q Consensus 55 ~~CPlC~~~V~~~~g~~pn~~v~~Hi~ 81 (190)
+.||+|++.|+ ...+++|+|
T Consensus 2 v~CPiC~~~v~-------~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVP-------ENLINSHLD 21 (26)
T ss_pred CcCCCCcCccc-------HHHHHHHHH
Confidence 46999999872 245778887
No 14
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=77.52 E-value=0.93 Score=26.18 Aligned_cols=12 Identities=42% Similarity=0.836 Sum_probs=10.5
Q ss_pred cceecccccccc
Q psy822 21 LPVKCDACLEMF 32 (190)
Q Consensus 21 LPf~C~~C~~~F 32 (190)
-||+|+.|++.|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 489999999987
No 15
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=74.75 E-value=1.2 Score=25.20 Aligned_cols=12 Identities=42% Similarity=1.107 Sum_probs=9.5
Q ss_pred ceeccccccccc
Q psy822 22 PVKCDACLEMFC 33 (190)
Q Consensus 22 Pf~C~~C~~~FC 33 (190)
||+|+.|++.|-
T Consensus 1 ~~~C~~C~~~F~ 12 (27)
T PF13912_consen 1 PFECDECGKTFS 12 (27)
T ss_dssp SEEETTTTEEES
T ss_pred CCCCCccCCccC
Confidence 688888888874
No 16
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=71.70 E-value=2.1 Score=28.53 Aligned_cols=34 Identities=26% Similarity=0.669 Sum_probs=19.3
Q ss_pred eecccccccccc----CCCCCCCccCCcccccccccccCCCCCCC
Q psy822 23 VKCDACLEMFCS----DHMSYVGHQCKSAARKDIQVPVCPLCNQP 63 (190)
Q Consensus 23 f~C~~C~~~FC~----eHr~~~~H~C~~~~~~d~~v~~CPlC~~~ 63 (190)
|+|++|++.|=. +|.. +.|. .+....+||+|...
T Consensus 3 f~CP~C~~~~~~~~L~~H~~-~~H~------~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCE-DEHR------SESKNVVCPICSSR 40 (54)
T ss_pred cCCCCCCCccCHHHHHHHHH-hHCc------CCCCCccCCCchhh
Confidence 789998884311 1111 1111 23446899999973
No 17
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=71.36 E-value=3.3 Score=27.32 Aligned_cols=33 Identities=27% Similarity=0.589 Sum_probs=21.7
Q ss_pred CCCcCCCCCcCc-----cCc--ccCcccCccccccCcCCC
Q psy822 98 NKCSVKNCKGKE-----LIP--VKCYQCAMNFCLKHRHPN 130 (190)
Q Consensus 98 ~~Cs~~~Ck~~~-----~~~--~~C~~C~~~FClkHR~p~ 130 (190)
..|+.++|.... ... +.|+.|+..||...+.+-
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 378888888752 223 899999999999998754
No 18
>KOG1813|consensus
Probab=70.76 E-value=2.1 Score=39.07 Aligned_cols=49 Identities=27% Similarity=0.476 Sum_probs=30.8
Q ss_pred CccccceeccccccccccCCCCC-CCccCCcccccccc-cccCCCCCCCcc
Q psy822 17 KLDFLPVKCDACLEMFCSDHMSY-VGHQCKSAARKDIQ-VPVCPLCNQPVP 65 (190)
Q Consensus 17 qlDFLPf~C~~C~~~FC~eHr~~-~~H~C~~~~~~d~~-v~~CPlC~~~V~ 65 (190)
-++-|||.|..|.+.|=..=++- ..|-|.....+..+ .+.|++|++.+.
T Consensus 236 D~~~~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 236 DIELLPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred CcccCCccccccccccccchhhcCCceeehhhhccccccCCcceecccccc
Confidence 35679999999999983322221 11225544344433 488999999765
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.40 E-value=7.1 Score=25.20 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=21.5
Q ss_pred cceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCC
Q psy822 21 LPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKR 68 (190)
Q Consensus 21 LPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~ 68 (190)
+.|+|..|+..|=.+-. .....||.|+.++.+..
T Consensus 2 ~~y~C~~CG~~~~~~~~--------------~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGREVELDEY--------------GTGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCEEEECCC--------------CCceECCCCCCeEEEcc
Confidence 45778887765533221 12568999999887543
No 20
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=58.89 E-value=7.1 Score=25.75 Aligned_cols=33 Identities=24% Similarity=0.699 Sum_probs=24.9
Q ss_pred CCCcCCCCCcCc-------cCcccCcccCccccccCcCCC
Q psy822 98 NKCSVKNCKGKE-------LIPVKCYQCAMNFCLKHRHPN 130 (190)
Q Consensus 98 ~~Cs~~~Ck~~~-------~~~~~C~~C~~~FClkHR~p~ 130 (190)
..|+.++|.... ...+.|+.|+..||...+.+-
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 458877886641 235889999999999998763
No 21
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=55.09 E-value=6.7 Score=35.49 Aligned_cols=52 Identities=27% Similarity=0.571 Sum_probs=31.9
Q ss_pred CCCCccccceecccc-----------ccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCC
Q psy822 14 TCKKLDFLPVKCDAC-----------LEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGE 70 (190)
Q Consensus 14 ~C~qlDFLPf~C~~C-----------~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~ 70 (190)
+|..|+-=-|+|..| +--||.+|...... .+.+ .+++.||.|+-.+...++.
T Consensus 163 sCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~----ky~k-~k~~PCPKCg~et~eTkdL 225 (314)
T PF06524_consen 163 SCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGF----KYEK-GKPIPCPKCGYETQETKDL 225 (314)
T ss_pred hhhhhhcccccccccccccchhhhheeeeehhhhhhhccc----cccc-CCCCCCCCCCCcccccccc
Confidence 444555555555544 45599999764431 1222 2688999999988755443
No 22
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=53.43 E-value=5.3 Score=27.28 Aligned_cols=26 Identities=27% Similarity=0.617 Sum_probs=13.5
Q ss_pred ccceeccccccccccCC---CCCCCccCC
Q psy822 20 FLPVKCDACLEMFCSDH---MSYVGHQCK 45 (190)
Q Consensus 20 FLPf~C~~C~~~FC~eH---r~~~~H~C~ 45 (190)
-..|+|..|++.||.|= ....-|+||
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred CCeEECCCCCCccccCcChhhhccccCCc
Confidence 36799999999999873 233466766
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=52.17 E-value=5.8 Score=21.40 Aligned_cols=8 Identities=38% Similarity=1.489 Sum_probs=3.6
Q ss_pred CCCCCCCc
Q psy822 57 CPLCNQPV 64 (190)
Q Consensus 57 CPlC~~~V 64 (190)
||.|++..
T Consensus 3 C~~C~~~f 10 (23)
T PF00096_consen 3 CPICGKSF 10 (23)
T ss_dssp ETTTTEEE
T ss_pred CCCCCCcc
Confidence 44444433
No 24
>PF06006 DUF905: Bacterial protein of unknown function (DUF905); InterPro: IPR009253 This family consists of several short hypothetical proteobacterial proteins of unknown function.; PDB: 2HJJ_A.
Probab=52.01 E-value=25 Score=25.65 Aligned_cols=37 Identities=22% Similarity=0.392 Sum_probs=17.7
Q ss_pred HHHHHHHhhhhhhhccccccccceeeEEEEEeeeeeeeCCCcEee
Q psy822 142 RNKALLKMKLWHELSNYQCKKHHLRLEIKVFYPTAVVCPNGTLVW 186 (190)
Q Consensus 142 ~~~a~~k~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (190)
+.+|.+-.....+---=-.+-.|.||.|. .++|++||
T Consensus 10 r~qA~aV~a~y~NV~IeDdqg~HfRlvvR--------d~~g~mvW 46 (70)
T PF06006_consen 10 REQAEAVAAQYRNVFIEDDQGTHFRLVVR--------DTEGQMVW 46 (70)
T ss_dssp HHHHHHHHHH-TTEEEES-SSS--EEEEE---------SS--EEE
T ss_pred HHHHHHHHHHhcceeeccCCCCeEEEEEE--------cCCCcEEE
Confidence 44454444433322222256789999876 68999998
No 25
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=51.27 E-value=10 Score=24.30 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=20.7
Q ss_pred ceeccccccccccCCCCCCCccCCcccccccccccCCCCCC
Q psy822 22 PVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQ 62 (190)
Q Consensus 22 Pf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~ 62 (190)
-|+|..|+..|=...... +...+.||.|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~-----------~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS-----------EDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcC-----------CCCCCcCCCCCC
Confidence 488999998886554321 123567999988
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=49.23 E-value=9.2 Score=37.61 Aligned_cols=11 Identities=36% Similarity=0.963 Sum_probs=8.4
Q ss_pred ceecccccccc
Q psy822 22 PVKCDACLEMF 32 (190)
Q Consensus 22 Pf~C~~C~~~F 32 (190)
++.|+.|++.|
T Consensus 453 H~~C~~Cgk~f 463 (567)
T PLN03086 453 HVHCEKCGQAF 463 (567)
T ss_pred CccCCCCCCcc
Confidence 46788888877
No 27
>PHA00616 hypothetical protein
Probab=48.96 E-value=5.4 Score=26.53 Aligned_cols=12 Identities=25% Similarity=0.514 Sum_probs=8.2
Q ss_pred ceeccccccccc
Q psy822 22 PVKCDACLEMFC 33 (190)
Q Consensus 22 Pf~C~~C~~~FC 33 (190)
||+|..||+.|-
T Consensus 1 pYqC~~CG~~F~ 12 (44)
T PHA00616 1 MYQCLRCGGIFR 12 (44)
T ss_pred CCccchhhHHHh
Confidence 567777777764
No 28
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.33 E-value=8.5 Score=24.04 Aligned_cols=16 Identities=19% Similarity=0.486 Sum_probs=10.6
Q ss_pred ccCCCCCCCccCCCCC
Q psy822 55 PVCPLCNQPVPTKRGE 70 (190)
Q Consensus 55 ~~CPlC~~~V~~~~g~ 70 (190)
++||-|+..-.++...
T Consensus 3 i~Cp~C~~~y~i~d~~ 18 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK 18 (36)
T ss_pred EECCCCCCEEeCCHHH
Confidence 5788888866655433
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=45.35 E-value=9.5 Score=19.97 Aligned_cols=8 Identities=38% Similarity=1.489 Sum_probs=3.3
Q ss_pred CCCCCCCc
Q psy822 57 CPLCNQPV 64 (190)
Q Consensus 57 CPlC~~~V 64 (190)
||+|++..
T Consensus 3 C~~C~~~~ 10 (24)
T PF13894_consen 3 CPICGKSF 10 (24)
T ss_dssp -SSTS-EE
T ss_pred CcCCCCcC
Confidence 55565544
No 30
>KOG2462|consensus
Probab=45.17 E-value=9.5 Score=34.42 Aligned_cols=60 Identities=25% Similarity=0.538 Sum_probs=37.6
Q ss_pred cceeccccccccc---------cCCCCCCCccCCc----ccc-----------cccccccCCCCCCCccCCCCCCcchhh
Q psy822 21 LPVKCDACLEMFC---------SDHMSYVGHQCKS----AAR-----------KDIQVPVCPLCNQPVPTKRGELPDFAV 76 (190)
Q Consensus 21 LPf~C~~C~~~FC---------~eHr~~~~H~C~~----~~~-----------~d~~v~~CPlC~~~V~~~~g~~pn~~v 76 (190)
||++|..|||.|= ..|.-.+.+.|+- +.+ .|+.-..|+.|+|...+. --+
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~------SyL 259 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK------SYL 259 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH------HHH
Confidence 7899999999885 3444456666652 111 244456788888766432 245
Q ss_pred cccccCCCCC
Q psy822 77 GLHIDNNCDS 86 (190)
Q Consensus 77 ~~Hi~~~C~~ 86 (190)
++|..++|..
T Consensus 260 nKH~ES~C~~ 269 (279)
T KOG2462|consen 260 NKHSESACLK 269 (279)
T ss_pred HHhhhhcccc
Confidence 6777777753
No 31
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=43.71 E-value=9.5 Score=23.83 Aligned_cols=16 Identities=19% Similarity=0.509 Sum_probs=11.1
Q ss_pred ccCCCCCCCccCCCCC
Q psy822 55 PVCPLCNQPVPTKRGE 70 (190)
Q Consensus 55 ~~CPlC~~~V~~~~g~ 70 (190)
++||-|+....++..+
T Consensus 3 i~CP~C~~~f~v~~~~ 18 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK 18 (37)
T ss_pred EECCCCCceEEcCHHH
Confidence 5799999877655433
No 32
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=43.59 E-value=17 Score=22.18 Aligned_cols=31 Identities=26% Similarity=0.562 Sum_probs=18.9
Q ss_pred eeccccccccccCCCCCCCccCCcccccccccccCCCCCCCc
Q psy822 23 VKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPV 64 (190)
Q Consensus 23 f~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V 64 (190)
|+|..|++.|=..... .+...+.||.|+..+
T Consensus 6 y~C~~Cg~~fe~~~~~-----------~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKI-----------SDDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEec-----------CCCCCCCCCCCCCcc
Confidence 6888888777433321 112356799998844
No 33
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.77 E-value=11 Score=35.60 Aligned_cols=26 Identities=38% Similarity=0.868 Sum_probs=21.2
Q ss_pred ccCCCCCCCccCCCCCCcchhhcccccCCCCCc
Q psy822 55 PVCPLCNQPVPTKRGELPDFAVGLHIDNNCDSD 87 (190)
Q Consensus 55 ~~CPlC~~~V~~~~g~~pn~~v~~Hi~~~C~~~ 87 (190)
+.||+|++.|+ ...|+.|++++|...
T Consensus 182 v~CPiC~~~~~-------~~~i~~Hld~~Cl~~ 207 (397)
T TIGR00599 182 VQCPICQQRMP-------EKAVERHLDSECLGS 207 (397)
T ss_pred ccCCCcccccC-------HHHHHHHHhccCCCC
Confidence 57999999885 447899999989753
No 34
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=42.43 E-value=15 Score=25.93 Aligned_cols=16 Identities=44% Similarity=1.072 Sum_probs=12.3
Q ss_pred cccccCCCCCCCccCC
Q psy822 52 IQVPVCPLCNQPVPTK 67 (190)
Q Consensus 52 ~~v~~CPlC~~~V~~~ 67 (190)
...|+||||+.+....
T Consensus 37 ~~~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVSG 52 (59)
T ss_pred CCCccCCCcCCccccc
Confidence 4579999999976533
No 35
>PHA02768 hypothetical protein; Provisional
Probab=41.77 E-value=11 Score=26.14 Aligned_cols=13 Identities=31% Similarity=0.840 Sum_probs=10.4
Q ss_pred ccceecccccccc
Q psy822 20 FLPVKCDACLEMF 32 (190)
Q Consensus 20 FLPf~C~~C~~~F 32 (190)
.|-|+|+.|++.|
T Consensus 3 ~~~y~C~~CGK~F 15 (55)
T PHA02768 3 LLGYECPICGEIY 15 (55)
T ss_pred ccccCcchhCCee
Confidence 5678888888887
No 36
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=40.29 E-value=12 Score=23.67 Aligned_cols=31 Identities=19% Similarity=0.610 Sum_probs=20.7
Q ss_pred ceeccccccccccCCCCCCCccCCcccccccccccCCCCCC
Q psy822 22 PVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQ 62 (190)
Q Consensus 22 Pf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~ 62 (190)
++.=-.|+-+||.+...... .....||+|++
T Consensus 14 ~~~l~~CgH~~C~~C~~~~~----------~~~~~CP~C~k 44 (44)
T PF14634_consen 14 RPRLTSCGHIFCEKCLKKLK----------GKSVKCPICRK 44 (44)
T ss_pred CeEEcccCCHHHHHHHHhhc----------CCCCCCcCCCC
Confidence 34445688888888765333 23567999975
No 37
>KOG1701|consensus
Probab=38.57 E-value=18 Score=34.77 Aligned_cols=47 Identities=23% Similarity=0.558 Sum_probs=38.5
Q ss_pred ccccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCcchhh
Q psy822 18 LDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELPDFAV 76 (190)
Q Consensus 18 lDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~pn~~v 76 (190)
||=.||+-+.=++++|.+-+. ++-+|.|-+|++||--..|+++.+.|
T Consensus 370 ldgipFtvd~~n~v~Cv~dfh------------~kfAPrCs~C~~PI~P~~G~~etvRv 416 (468)
T KOG1701|consen 370 LDGIPFTVDSQNNVYCVPDFH------------KKFAPRCSVCGNPILPRDGKDETVRV 416 (468)
T ss_pred cCCccccccCCCceeeehhhh------------hhcCcchhhccCCccCCCCCcceEEE
Confidence 788888888888888887654 56789999999999988899876544
No 38
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=38.29 E-value=20 Score=25.24 Aligned_cols=42 Identities=24% Similarity=0.429 Sum_probs=29.2
Q ss_pred ccccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCc
Q psy822 18 LDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELP 72 (190)
Q Consensus 18 lDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~p 72 (190)
-.||-.+|+.|++.-- ..++-..++.|+.|+..+..|.|...
T Consensus 7 S~F~~VkCp~C~n~q~-------------vFsha~t~V~C~~Cg~~L~~PtGGKa 48 (59)
T PRK00415 7 SRFLKVKCPDCGNEQV-------------VFSHASTVVRCLVCGKTLAEPTGGKA 48 (59)
T ss_pred CeEEEEECCCCCCeEE-------------EEecCCcEEECcccCCCcccCCCcce
Confidence 3588899988865321 11123457889999999998887654
No 39
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=37.69 E-value=15 Score=22.46 Aligned_cols=34 Identities=15% Similarity=0.272 Sum_probs=17.8
Q ss_pred eeccccccccccCCCCCCCccCCcccccccccccCCCCCCCcc
Q psy822 23 VKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVP 65 (190)
Q Consensus 23 f~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~ 65 (190)
++|+.|+..|=.+-... .. +...+.||.|+.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~--------~~-~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL--------GA-NGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc--------CC-CCCEEECCCCCCEEE
Confidence 56777776664442210 01 112466888877653
No 40
>KOG4739|consensus
Probab=35.85 E-value=23 Score=31.21 Aligned_cols=37 Identities=30% Similarity=0.654 Sum_probs=26.4
Q ss_pred ccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCC
Q psy822 20 FLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKR 68 (190)
Q Consensus 20 FLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~ 68 (190)
=-||.=..|..+||..+..... .| +||+|.++|.+..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~--------~~----~C~lCkk~ir~i~ 51 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASS--------PD----VCPLCKKSIRIIQ 51 (233)
T ss_pred CCceeeeechhhhhhhhcccCC--------cc----ccccccceeeeee
Confidence 3456667899999999875221 22 8999999987553
No 41
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=34.55 E-value=27 Score=22.67 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=19.1
Q ss_pred eeccccccccccCCCCCCCccCCcccccccccccCCCCCC
Q psy822 23 VKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQ 62 (190)
Q Consensus 23 f~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~ 62 (190)
|+|..|+..|=..... . +...+.||.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~-~----------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKM-S----------DDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEec-C----------CCCCCCCCCCCC
Confidence 6888888877554322 1 123467999997
No 42
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.90 E-value=19 Score=33.34 Aligned_cols=63 Identities=27% Similarity=0.535 Sum_probs=44.1
Q ss_pred CCCCCCCCCCCcCCCCCccccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCcch
Q psy822 1 MEFPHLGKHCSIETCKKLDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELPDF 74 (190)
Q Consensus 1 MEf~diG~hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~pn~ 74 (190)
|.|++|.-.|- .|+-|---|.+=..|+..||.|-..- ++-+.| .+||-|++.=.+..+..||+
T Consensus 268 ~~~~~i~LkCp--lc~~Llrnp~kT~cC~~~fc~eci~~------al~dsD---f~CpnC~rkdvlld~l~pD~ 330 (427)
T COG5222 268 MQPPNISLKCP--LCHCLLRNPMKTPCCGHTFCDECIGT------ALLDSD---FKCPNCSRKDVLLDGLTPDI 330 (427)
T ss_pred cCCCCccccCc--chhhhhhCcccCccccchHHHHHHhh------hhhhcc---ccCCCcccccchhhccCccH
Confidence 78899999998 88888888888888999999886531 121222 35788887544455555554
No 43
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=32.28 E-value=23 Score=25.63 Aligned_cols=42 Identities=24% Similarity=0.412 Sum_probs=30.0
Q ss_pred ccccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCc
Q psy822 18 LDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELP 72 (190)
Q Consensus 18 lDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~p 72 (190)
--||-.+|..|++.-+-- ..-..++.|+.|+..+..|.|.-.
T Consensus 15 s~Fl~VkCpdC~N~q~vF-------------shast~V~C~~CG~~l~~PTGGka 56 (67)
T COG2051 15 SRFLRVKCPDCGNEQVVF-------------SHASTVVTCLICGTTLAEPTGGKA 56 (67)
T ss_pred ceEEEEECCCCCCEEEEe-------------ccCceEEEecccccEEEecCCCeE
Confidence 359999999998764321 112357889999999988876653
No 44
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=29.98 E-value=18 Score=24.06 Aligned_cols=10 Identities=50% Similarity=1.504 Sum_probs=5.3
Q ss_pred cCCCCCCCcc
Q psy822 56 VCPLCNQPVP 65 (190)
Q Consensus 56 ~CPlC~~~V~ 65 (190)
.||+|++++.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 8999999774
No 45
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=28.52 E-value=40 Score=26.14 Aligned_cols=26 Identities=31% Similarity=0.798 Sum_probs=19.3
Q ss_pred CCCcCCCCCcC--cc--CcccCcccCcccccc
Q psy822 98 NKCSVKNCKGK--EL--IPVKCYQCAMNFCLK 125 (190)
Q Consensus 98 ~~Cs~~~Ck~~--~~--~~~~C~~C~~~FClk 125 (190)
..|.- |+++ .+ .|++|++||..|=+.
T Consensus 10 R~Cp~--CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPS--CGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCC--CcchhccCCCCCccCCCCCCccCcc
Confidence 46754 8876 33 589999999998555
No 46
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=27.84 E-value=37 Score=28.33 Aligned_cols=39 Identities=23% Similarity=0.453 Sum_probs=25.6
Q ss_pred eccccccccc-------cCCCCCCCccCCcccccccccccCCCCCCCccC
Q psy822 24 KCDACLEMFC-------SDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPT 66 (190)
Q Consensus 24 ~C~~C~~~FC-------~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~ 66 (190)
.|..|+..+. .|| +|.|.......++-+.|+.||..+-.
T Consensus 22 ~CaiC~~~l~~~~~~~~vDH----DH~l~g~~TG~VRGLLC~~CN~~lG~ 67 (157)
T PHA02565 22 ICPLCKRELDGDVSKNHLDH----DHELNGPNAGRVRGLLCNLCNALEGQ 67 (157)
T ss_pred cCCCCCCccCCCccccccCC----CCCCCCcccccccccCchhhhhhhhh
Confidence 3556666554 444 56665444556789999999996653
No 47
>smart00355 ZnF_C2H2 zinc finger.
Probab=27.39 E-value=25 Score=18.29 Aligned_cols=6 Identities=50% Similarity=1.647 Sum_probs=2.8
Q ss_pred CCCCCC
Q psy822 57 CPLCNQ 62 (190)
Q Consensus 57 CPlC~~ 62 (190)
|+.|++
T Consensus 3 C~~C~~ 8 (26)
T smart00355 3 CPECGK 8 (26)
T ss_pred CCCCcc
Confidence 444444
No 48
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=27.32 E-value=16 Score=24.01 Aligned_cols=26 Identities=35% Similarity=0.820 Sum_probs=17.1
Q ss_pred cccCCC--CCCCccCCCCCCcchhhcccccCCCCC
Q psy822 54 VPVCPL--CNQPVPTKRGELPDFAVGLHIDNNCDS 86 (190)
Q Consensus 54 v~~CPl--C~~~V~~~~g~~pn~~v~~Hi~~~C~~ 86 (190)
.+.||. |++.|+.. .++.|+++.|..
T Consensus 9 ~v~C~~~cc~~~i~r~-------~l~~H~~~~C~~ 36 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRK-------ELDDHLENECPK 36 (60)
T ss_dssp EEE-TT--S-BEEECC-------CHHHHHHTTSTT
T ss_pred EeeCCCCCcccceeHH-------HHHHHHHccCCC
Confidence 467988 77766532 478899888864
No 49
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.25 E-value=33 Score=28.93 Aligned_cols=11 Identities=55% Similarity=1.509 Sum_probs=9.6
Q ss_pred cccCCCCCCCc
Q psy822 54 VPVCPLCNQPV 64 (190)
Q Consensus 54 v~~CPlC~~~V 64 (190)
-|.||+|+.||
T Consensus 154 RP~CPlCg~Pl 164 (171)
T PF11290_consen 154 RPPCPLCGEPL 164 (171)
T ss_pred CCCCCCCCCCC
Confidence 47899999986
No 50
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=26.17 E-value=50 Score=23.47 Aligned_cols=14 Identities=36% Similarity=0.769 Sum_probs=11.5
Q ss_pred ccccCCCCCCCccC
Q psy822 53 QVPVCPLCNQPVPT 66 (190)
Q Consensus 53 ~v~~CPlC~~~V~~ 66 (190)
.++.||.|++++..
T Consensus 5 ~~v~CP~C~k~~~w 18 (62)
T PRK00418 5 ITVNCPTCGKPVEW 18 (62)
T ss_pred ccccCCCCCCcccc
Confidence 46789999998864
No 51
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=25.92 E-value=51 Score=19.32 Aligned_cols=18 Identities=22% Similarity=0.610 Sum_probs=12.2
Q ss_pred CCcC-ccCcccCcccCccc
Q psy822 105 CKGK-ELIPVKCYQCAMNF 122 (190)
Q Consensus 105 Ck~~-~~~~~~C~~C~~~F 122 (190)
|.+. ......|+.||-.|
T Consensus 6 C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 6 CGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred CcCCchhhcCcCCCCCCCC
Confidence 6655 33456799998776
No 52
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=24.98 E-value=39 Score=20.39 Aligned_cols=19 Identities=26% Similarity=0.730 Sum_probs=12.8
Q ss_pred CCCCccccceecccccccccc
Q psy822 14 TCKKLDFLPVKCDACLEMFCS 34 (190)
Q Consensus 14 ~C~qlDFLPf~C~~C~~~FC~ 34 (190)
.|+. +=.|+|+.|+..+|+
T Consensus 7 vC~~--~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 7 VCGN--PAKYRCPRCGARYCS 25 (30)
T ss_dssp SSSS--EESEE-TTT--EESS
T ss_pred cCcC--CCEEECCCcCCceeC
Confidence 4777 778899999988885
No 53
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=24.59 E-value=25 Score=29.84 Aligned_cols=23 Identities=17% Similarity=0.592 Sum_probs=0.0
Q ss_pred ccccCCCCCCCccCCCCCCcchhhcccccC
Q psy822 53 QVPVCPLCNQPVPTKRGELPDFAVGLHIDN 82 (190)
Q Consensus 53 ~v~~CPlC~~~V~~~~g~~pn~~v~~Hi~~ 82 (190)
...+||+|++.||.. -|++|++-
T Consensus 167 ~~~~cPitGe~IP~~-------e~~eHmRi 189 (229)
T PF12230_consen 167 KMIICPITGEMIPAD-------EMDEHMRI 189 (229)
T ss_dssp ------------------------------
T ss_pred ccccccccccccccc-------cccccccc
Confidence 457899999999855 45667653
No 54
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=24.06 E-value=36 Score=19.91 Aligned_cols=8 Identities=50% Similarity=1.202 Sum_probs=4.6
Q ss_pred CCCCCCCc
Q psy822 57 CPLCNQPV 64 (190)
Q Consensus 57 CPlC~~~V 64 (190)
|.+|++.+
T Consensus 6 C~~C~~~~ 13 (35)
T smart00451 6 CKLCNVTF 13 (35)
T ss_pred ccccCCcc
Confidence 56666644
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.05 E-value=34 Score=19.61 Aligned_cols=10 Identities=40% Similarity=0.913 Sum_probs=8.5
Q ss_pred ccCcccCccc
Q psy822 113 VKCYQCAMNF 122 (190)
Q Consensus 113 ~~C~~C~~~F 122 (190)
+.|+.|++.|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5799999988
No 56
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.90 E-value=44 Score=24.03 Aligned_cols=17 Identities=29% Similarity=0.470 Sum_probs=13.0
Q ss_pred ccccccCCCCCCCccCC
Q psy822 51 DIQVPVCPLCNQPVPTK 67 (190)
Q Consensus 51 d~~v~~CPlC~~~V~~~ 67 (190)
++....||.|+++|...
T Consensus 4 ~~~~v~CP~Cgkpv~w~ 20 (65)
T COG3024 4 LRITVPCPTCGKPVVWG 20 (65)
T ss_pred ccccccCCCCCCccccc
Confidence 34566799999998753
No 57
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=23.78 E-value=39 Score=28.66 Aligned_cols=11 Identities=55% Similarity=1.543 Sum_probs=9.8
Q ss_pred cccCCCCCCCc
Q psy822 54 VPVCPLCNQPV 64 (190)
Q Consensus 54 v~~CPlC~~~V 64 (190)
-|.||+|++||
T Consensus 156 RP~CPlCg~Pl 166 (177)
T TIGR03847 156 RPPCPLCGRPI 166 (177)
T ss_pred CCCCCCCCCCC
Confidence 47899999988
No 58
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=23.55 E-value=52 Score=28.98 Aligned_cols=38 Identities=24% Similarity=0.586 Sum_probs=25.0
Q ss_pred ccccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCC
Q psy822 18 LDFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQP 63 (190)
Q Consensus 18 lDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~ 63 (190)
..+..++|..|++.|=.+... ....+..+|.||.|+.+
T Consensus 118 Gsl~~~~C~~C~~~~~~~~~~--------~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 118 GSLKRVRCSKCGNQYYDEDVI--------KFIEDGLIPRCPKCGGP 155 (250)
T ss_pred cceeeeEeCCCcCccchhhhh--------hhcccCCCCcCccCCCc
Confidence 356788899998776544311 11123468999999994
No 59
>KOG2462|consensus
Probab=22.51 E-value=38 Score=30.64 Aligned_cols=25 Identities=32% Similarity=0.716 Sum_probs=21.2
Q ss_pred ceeccccccccc---------cCCCCCCCccCCc
Q psy822 22 PVKCDACLEMFC---------SDHMSYVGHQCKS 46 (190)
Q Consensus 22 Pf~C~~C~~~FC---------~eHr~~~~H~C~~ 46 (190)
||.|.+|++.|= .-|-..+.|.|..
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~ 248 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPR 248 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCccccCcc
Confidence 999999999994 4678888899874
No 60
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=22.43 E-value=52 Score=21.35 Aligned_cols=25 Identities=32% Similarity=0.727 Sum_probs=16.5
Q ss_pred CCCC-cccc--ceeccccccccccCCCC
Q psy822 14 TCKK-LDFL--PVKCDACLEMFCSDHMS 38 (190)
Q Consensus 14 ~C~q-lDFL--Pf~C~~C~~~FC~eHr~ 38 (190)
.|++ +.++ ...|..|++.||.++..
T Consensus 7 ~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~ 34 (57)
T cd00065 7 GCGKPFTLTRRRHHCRNCGRIFCSKCSS 34 (57)
T ss_pred ccCccccCCccccccCcCcCCcChHHcC
Confidence 5543 4444 46788888888886654
No 61
>PLN00209 ribosomal protein S27; Provisional
Probab=22.38 E-value=52 Score=24.87 Aligned_cols=41 Identities=24% Similarity=0.490 Sum_probs=28.8
Q ss_pred cccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCc
Q psy822 19 DFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELP 72 (190)
Q Consensus 19 DFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~p 72 (190)
-||-++|..|.+.-- .......++.|..|+.++..|.|.-.
T Consensus 33 ~Fm~VkCp~C~n~q~-------------VFShA~t~V~C~~Cg~~L~~PTGGKa 73 (86)
T PLN00209 33 FFMDVKCQGCFNITT-------------VFSHSQTVVVCGSCQTVLCQPTGGKA 73 (86)
T ss_pred EEEEEECCCCCCeeE-------------EEecCceEEEccccCCEeeccCCCCe
Confidence 588888988865411 11233467889999999998887764
No 62
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=21.81 E-value=46 Score=18.80 Aligned_cols=21 Identities=14% Similarity=0.476 Sum_probs=12.6
Q ss_pred cCCCCCCCccCCCCCCcchhhcccccC
Q psy822 56 VCPLCNQPVPTKRGELPDFAVGLHIDN 82 (190)
Q Consensus 56 ~CPlC~~~V~~~~g~~pn~~v~~Hi~~ 82 (190)
.|++|++... -..++++|+.+
T Consensus 3 ~C~~C~k~f~------~~~~~~~H~~s 23 (27)
T PF12171_consen 3 YCDACDKYFS------SENQLKQHMKS 23 (27)
T ss_dssp BBTTTTBBBS------SHHHHHCCTTS
T ss_pred CcccCCCCcC------CHHHHHHHHcc
Confidence 4777777553 23466777653
No 63
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.72 E-value=50 Score=22.41 Aligned_cols=33 Identities=21% Similarity=0.512 Sum_probs=21.6
Q ss_pred cceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCC
Q psy822 21 LPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTK 67 (190)
Q Consensus 21 LPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~ 67 (190)
+-|+|..|++.| ........+.||.|+--|-+.
T Consensus 5 ~~Y~C~~Cg~~~--------------~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 5 MEYKCARCGREV--------------ELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred EEEEhhhcCCee--------------ehhhccCceeCCCCCcEEEEe
Confidence 347888888887 011234567899998877544
No 64
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=21.52 E-value=56 Score=24.68 Aligned_cols=41 Identities=22% Similarity=0.442 Sum_probs=28.9
Q ss_pred cccceeccccccccccCCCCCCCccCCcccccccccccCCCCCCCccCCCCCCc
Q psy822 19 DFLPVKCDACLEMFCSDHMSYVGHQCKSAARKDIQVPVCPLCNQPVPTKRGELP 72 (190)
Q Consensus 19 DFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~d~~v~~CPlC~~~V~~~~g~~p 72 (190)
-||-++|..|.+.-- ..++...++.|..|+.++..|.|...
T Consensus 32 ~Fm~VkCp~C~n~q~-------------VFShA~t~V~C~~Cg~~L~~PTGGKa 72 (85)
T PTZ00083 32 YFMDVKCPGCSQITT-------------VFSHAQTVVLCGGCSSQLCQPTGGKA 72 (85)
T ss_pred eEEEEECCCCCCeeE-------------EEecCceEEEccccCCEeeccCCCCe
Confidence 488888888865411 11233467889999999998887764
No 65
>TIGR02174 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam.
Probab=21.51 E-value=84 Score=22.07 Aligned_cols=27 Identities=37% Similarity=0.414 Sum_probs=16.0
Q ss_pred hhhhhccccccccceeeEEEEEeeeeeeeCCCcEeeec
Q psy822 151 LWHELSNYQCKKHHLRLEIKVFYPTAVVCPNGTLVWDF 188 (190)
Q Consensus 151 ~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (190)
+|.+..++ |-..=..||.| ||.|||+-
T Consensus 29 ~~v~~~~~--~~~~G~Fev~~---------~g~~v~sk 55 (72)
T TIGR02174 29 LEIEGENT--PPTTGAFEVTV---------NGQLVWSK 55 (72)
T ss_pred CeeEEeee--cCCCcEEEEEE---------CCEEEEEe
Confidence 34444443 33444556555 99999984
No 66
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.06 E-value=77 Score=25.13 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=26.5
Q ss_pred cceeccccccccccC--CCC------CCCccCCcccccccccccCCCCCCC-ccCCCCCC
Q psy822 21 LPVKCDACLEMFCSD--HMS------YVGHQCKSAARKDIQVPVCPLCNQP-VPTKRGEL 71 (190)
Q Consensus 21 LPf~C~~C~~~FC~e--Hr~------~~~H~C~~~~~~d~~v~~CPlC~~~-V~~~~g~~ 71 (190)
.-++|..|+..|=.+ |+. ..-|-=|... .....||.|+.. +.+..|..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~CP~Cgs~~~~i~~G~e 125 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVV---HAFLKCPKCGSRDFEIVKGRG 125 (135)
T ss_pred eEEECCCCCCEEeccccccccccccccccccccccc---ccCcCCcCCCCCCcEEecCce
Confidence 458899999888665 221 1122222211 223569999875 55555554
No 67
>PHA00732 hypothetical protein
Probab=20.91 E-value=41 Score=24.50 Aligned_cols=12 Identities=25% Similarity=0.315 Sum_probs=9.2
Q ss_pred ceeccccccccc
Q psy822 22 PVKCDACLEMFC 33 (190)
Q Consensus 22 Pf~C~~C~~~FC 33 (190)
||+|+.|++.|=
T Consensus 1 py~C~~Cgk~F~ 12 (79)
T PHA00732 1 MFKCPICGFTTV 12 (79)
T ss_pred CccCCCCCCccC
Confidence 678888888873
No 68
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=20.89 E-value=69 Score=19.49 Aligned_cols=16 Identities=19% Similarity=0.717 Sum_probs=13.6
Q ss_pred CcccCcccCccccccC
Q psy822 111 IPVKCYQCAMNFCLKH 126 (190)
Q Consensus 111 ~~~~C~~C~~~FClkH 126 (190)
..+.|+.|+...|.+|
T Consensus 15 T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVEP 30 (32)
T ss_pred eEEEccCCCCcccCCC
Confidence 5678999999999887
No 69
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.85 E-value=89 Score=18.81 Aligned_cols=8 Identities=50% Similarity=1.290 Sum_probs=5.9
Q ss_pred ccCCCCCC
Q psy822 55 PVCPLCNQ 62 (190)
Q Consensus 55 ~~CPlC~~ 62 (190)
-.||+|+.
T Consensus 18 ~~CP~Cg~ 25 (33)
T cd00350 18 WVCPVCGA 25 (33)
T ss_pred CcCcCCCC
Confidence 36888876
No 70
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.82 E-value=76 Score=30.36 Aligned_cols=22 Identities=36% Similarity=0.783 Sum_probs=17.0
Q ss_pred CCCcCCCCCcCccCcccCcccCcc
Q psy822 98 NKCSVKNCKGKELIPVKCYQCAMN 121 (190)
Q Consensus 98 ~~Cs~~~Ck~~~~~~~~C~~C~~~ 121 (190)
-+|.+ |+.....+-.|+.|+..
T Consensus 241 l~Ch~--Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 241 LRCHY--CGYQEPIPKTCPQCGSE 262 (505)
T ss_pred EEcCC--CcCcCCCCCCCCCCCCC
Confidence 46777 88888788889988763
No 71
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=20.13 E-value=20 Score=23.82 Aligned_cols=9 Identities=56% Similarity=1.464 Sum_probs=3.0
Q ss_pred ccCCCCCCC
Q psy822 55 PVCPLCNQP 63 (190)
Q Consensus 55 ~~CPlC~~~ 63 (190)
-.||+|+++
T Consensus 42 W~CPiC~~~ 50 (50)
T PF02891_consen 42 WKCPICNKP 50 (50)
T ss_dssp -B-TTT---
T ss_pred eECcCCcCc
Confidence 457777764
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.02 E-value=57 Score=25.70 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=13.1
Q ss_pred ceeccccccccccCC
Q psy822 22 PVKCDACLEMFCSDH 36 (190)
Q Consensus 22 Pf~C~~C~~~FC~eH 36 (190)
.|+|..|++.||.|=
T Consensus 81 ~y~C~~C~~~FC~dC 95 (112)
T TIGR00622 81 RYVCAVCKNVFCVDC 95 (112)
T ss_pred ceeCCCCCCcccccc
Confidence 588999999999775
Done!